I found this site the other day and I noticed that I have been seeing fewer and fewer really bright, bold, what I would describe as highlighter-esque colors these days in user interfaces that use flat design. Is there a reason for that? What should I take into consideration, if anything, when picking a colorscheme for site or app that uses a flat UI?
The 'flat design' aesthetic tends to favor large blocks of solid colors. If all of your colors are 'highlighter-esque' then you just end up with an incredibly busy UI where nothing stands out as they are all competing equally for your attention.
Intense vibrant colors--in UI design, at least--are there to draw attention so should only be used sparingly...just as you would with a true highlighter.
Else, you end up with a hot dog stand:
The answer doesn't depend on wether its flat or 3D because bright "highlighteresque" colors are harsh to the eyes, hard to read, and don't comply with usability guidelines for people with color blindness et. al. As an accent color they are fine but large swaths wouldn't be advisable nor would it be advised to place text on top of that sort of interface. As always context is everything but in light of the question. Not advised.
Harsh colors are one of those things that break through the unconscious into conscious awareness as an annoyance when in an interface. In other words, some UI choices, like counterintuitive navigation, fatigue users and they might not know the culprit. However, people usually speak up, knowing exactly why they don't enjoy an interface when it comes to the color scheme. So the palette will naturally tend toward more soothing colors in further iterations.
In addition, by not using harsh colors in your main palette, you can get people's attention when you need to by injecting a bold color occasionally for promotional or warning purposes.
You ask what considerations to keep in mind when developing your color scheme.
I like playing around in Illustrator to find 5 colors that will serve me well. You can also use online color resources like colourlovers.com and kuler.adobe.com. These are good starting places - but then you'll need to adjust them when you bring these colors into your actual UI and fonts.
I usually end up with 3-5 main palette colors and a handful of system and secondary colors.